PCA

Question: should we correct for batch?

Batch correction for HeLa cells: definitely.
Batch correction for HEK cells: maybe not necessary. Let’s compare both DEAs.

DEA

check results

##   let-7a    lsy-6    miR-1  miR-124  miR-137  miR-139  miR-143  miR-144 
##     2724     1601     5311     4618     3344      988      403      268 
##  miR-153  miR-155  miR-182 miR-199a  miR-204  miR-205 miR-216b  miR-223 
##     2121     1949     1987     1535      843     1068     1152     1503 
##    miR-7 
##     3174
##  miR-122  miR-133  miR-138  miR-145  miR-184 miR-190a miR-200b miR-216a 
##      419      552     2937      793      109      711     1080      300 
##  miR-217 miR-219a  miR-375 miR-451a 
##      420      379      718      132
##  miR-122  miR-133  miR-138  miR-145  miR-184 miR-190a miR-200b miR-216a 
##      274      377     1967      430       82      412      742      216 
##  miR-217 miR-219a  miR-375 miR-451a 
##      305      292      488       90
## [1] 486
## [1] 341
##            b_in_nb   nb_in_b
## miR-122  0.6539379 1.0000000
## miR-133  0.6829710 1.0000000
## miR-138  0.6690501 0.9989832
## miR-145  0.5422446 1.0000000
## miR-184  0.7522936 1.0000000
## miR-190a 0.5794655 1.0000000
## miR-200b 0.6861111 0.9986523
## miR-216a 0.7200000 1.0000000
## miR-217  0.7214286 0.9934426
## miR-219a 0.7651715 0.9931507
## miR-375  0.6796657 1.0000000
## miR-451a 0.6818182 1.0000000

We get more significant results with the batch corrected HEK DEA & almost all significant tx of the batch uncorrected HEK DEA are present in the corrected one. We thus choose the batch corrected version.